Gene-regulatory network analysis of ankylosing spondylitis with a single-cell chromatin accessible assay

Haiyan Yu,Donge Tang,Lianghong Yin,Weier Dai,Hongwei Wu,Dongzhou Liu,Xiaoping Hong,Chengxin Zhu,Yong Dai,Fengping Zheng

doi:10.1038/s41598-020-76574-5

Abstract

A detailed understanding of the gene-regulatory network in ankylosing spondylitis (AS) is vital for elucidating the mechanisms of AS pathogenesis. Assaying transposase-accessible chromatin in single cell sequencing (scATAC-seq) is a suitable method for revealing such networks. Thus, scATAC-seq was applied to define the landscape of active regulatory DNA in AS. As a result, there was a significant change in the percent of CD8+ T cells in PBMCs, and 37 differentially accessible transcription factor (TF) motifs were identified. T cells, monocytes-1 and dendritic cells were found to be crucial for the IL-17 signaling pathway and TNF signaling pathway, since they had 73 potential target genes regulated by 8 TF motifs with decreased accessibility in AS. Moreover, natural killer cells were involved in AS by increasing the accessibility to TF motifs TEAD1 and JUN to induce cytokine-cytokine receptor interactions. In addition, CD4+ T cells and CD8+ T cells may be vital for altering host immune functions through increasing the accessibility of TF motifs NR1H4 and OLIG (OLIGI and OLIG2), respectively. These results explain clear gene regulatory variation in PBMCs from AS patients, providing a foundational framework for the study of personal regulomes and delivering insights into epigenetic therapy.

Highlights

A detailed understanding of the gene-regulatory network in ankylosing spondylitis (AS) is vital for elucidating the mechanisms of AS pathogenesis
In the AS_PBMC library, 19.12% of the fragments were assigned to TSSs, 13.01% were mapped to enhancer regions, 11.77% were linked to promoter regions, 22.36% were in nucleosome-free regions, 70.60% were mapped to a single nucleosome, and the fraction of total read pairs mapped confidently to the genome was 86.59%
Since the immune cells circulate in the body through blood, research on peripheral blood mononuclear cells (PBMCs) contributes to finding out markers for diagnosis and target therapy

Summary

Introduction

A detailed understanding of the gene-regulatory network in ankylosing spondylitis (AS) is vital for elucidating the mechanisms of AS pathogenesis. Assaying transposase-accessible chromatin in single cell sequencing (scATAC-seq) was devolved to map open chromatin regions and identify regulatory regions[5] This method is simple and sensitive and capable of recognizing different cell types, including subtle and rare cell subtypes, and it can reveal celltype-specific regulatory regions and explore related transcription factors (TFs). The single-cell chromatin assay has successfully mapped the regulatory landscape of adult mouse tissues, characterized 85 distinct chromatin patterns, annotated key regulators in diverse mammalian cell types and identified cell types underlying common human traits and d iseases[6] Another group used scATAC-seq to study the mouse forebrain at eight developmental stages, and they found cell-type-specific transcriptional regulation and provided insight.

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